Investigating the drivers of microbial community composition in reef-building corals

Epstein, Hannah Elizabeth (2018) Investigating the drivers of microbial community composition in reef-building corals. PhD thesis, James Cook University.

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The abundance and diversity of microbes in corals are indicative of an intricate coexistence between the metazoan host and these unicellular partners. An increasing number of studies have identified explicit functions that some microbes perform in the coral holobiont, ranging from nutrient cycling to immunity. Rapid climate change can affect coral-associated microbial symbioses through negative shifts in microbial community structure (i.e., dysbiosis) that can lead to coral disease and mortality. Alternately, microbes may contribute to holobiont resilience by rapidly adapting to new environmental regimes and may provide the coral with an uninterrupted suite of functions. To understand whether shifts in the microbiome as a result of environmental change will be positive or negative, the drivers of natural variations in community composition must be understood. This thesis is focused on investigating and identifying some of the drivers of microbial community composition in corals, specifically of the Symbiodiniaceae and bacterial communities, to improve our ability to predict the impacts of climate change on corals, and to provide critical baseline data that may be used to inform the development of the microbial-driven restoration technique of microbiome engineering. Using both survey and experimental methods, the specific aims of this thesis were to 1) review the literature on microbiome engineering and identify new research directions that will aid the development of microbiome engineering in corals, 2) investigate the long-term seasonal variation in coral-associated microbiomes, 3) examine the effects of a temperature anomaly on the stability of the coral microbiome and 4) determine the drivers of microbial community establishment in coral offspring.

Obtaining direction from established research on microbiome engineering in biological systems such as plants, human health and waste water treatment, Chapter 2 identified three main research priorities that would not only provide a foundation of knowledge for developing coral-specific microbiome engineering tools, but also further the coral microbial ecology field in general. These research priorities were to 1) determine the variable and stable partners of the microbiome, 2) identify microbial function and 3) use experimental methods to determine key microbial players and assess the feasibility of manipulation methods. The remaining data chapters of this thesis focused on addressing some of the knowledge gaps associated with the natural variability and stability of the microbiome to identify what may be driving patterns of microbial community composition using 16S rRNA gene and ITS2 spacer metabarcoding for bacteria and Symbiodiniaceae, respectively. In Chapter 3, twelve tagged colonies each of two species of Acropora corals at two mid-shelf reefs on the Great Barrier Reef (GBR) were sampled over two years to examine whether temporal changes in the coral microbiome reflect cyclical seasonal cycles, and whether there is evidence for coral host-specificity or location effects on microbiome composition. Findings from this chapter confirm that the coral microbiome is complex and dynamic, but does not reflect seasonal cycles, at least not in the species and reefs studied here. Coral microbiomes also varied within coral species according to reef, suggesting that reef environment or location further drives microbial community composition. In Chapter 4, ten tagged colonies of Pocillopora acuta, a comparatively bleaching resistant coral, were visually inspected and sampled during the 2016 thermal anomaly in the northern and central GBR that resulted in widespread bleaching. Despite experiencing higher than average temperatures and two-degree heating weeks, these corals exhibited no visible signs of bleaching and little variation in their bacterial and Symbiodiniaceae communities through time. Indicator analyses identified microbes that could harbor beneficial properties for thermal tolerance, but future functional studies will be necessary for validation. Finally, Chapter 5 describes the results of a manipulative experiment to determine the influence of parents and environment on the establishment of the microbiome in coral offspring of the species Pocillopora damicornis. Findings provided evidence for mixed mode transmission for both bacteria and Symbiodiniaceae, with offspring sharing a small number of microbial taxa with their parents and some with the water column. Microbial communities in early coral life stages were characterized by high variability and dispersion in comparison to parents, suggesting that they shape their microbial communities throughout ontogeny (i.e., "winnowing").

This thesis has identified both host and environmental factors were crucial drivers of the coral microbiome. For some coral species in certain locations, shifts in microbial community composition may provide adaptive benefits, while for others, they may cause bleaching, disease or mortality. The effects of these shifts for the coral host, whether positive or negative, are likely host specific, reliant on their geographic location and contingent on the severity of the stress events they witness. While this may pose a challenge for implementing long-term microbial manipulations intended for reef restoration, short-term probiotic treatments for bioremediation or immediate prevention should be investigated further. Future empirical work on microbial function and the ability for the microbiome to facilitate climate resilience in corals is essential.

Item ID: 56861
Item Type: Thesis (PhD)
Keywords: microbiome engineering, coral, climate change, thermal stress, climate resilience, coral reefs, Symbiodiniaceae, Great Barrier Reef, Pocillopora acuta, Pocillopora damicornis
Copyright Information: Copyright © 2018 Hannah Elizabeth Epstein
Date Deposited: 15 Jan 2019 05:24
FoR Codes: 05 ENVIRONMENTAL SCIENCES > 0501 Ecological Applications > 050101 Ecological Impacts of Climate Change @ 30%
06 BIOLOGICAL SCIENCES > 0605 Microbiology > 060599 Microbiology not elsewhere classified @ 35%
06 BIOLOGICAL SCIENCES > 0602 Ecology > 060205 Marine and Estuarine Ecology (incl Marine Ichthyology) @ 35%
SEO Codes: 96 ENVIRONMENT > 9608 Flora, Fauna and Biodiversity > 960808 Marine Flora, Fauna and Biodiversity @ 50%
97 EXPANDING KNOWLEDGE > 970106 Expanding Knowledge in the Biological Sciences @ 50%
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